SOFA 2010 Retrospective

Highlights

• 3379 commits from 40 contributors added 200K new lines of code in the codebase.
• Scientific papers using SOFA were published in highly visible conferences and journals, including one SIGGRAPH paper, two at MICCAI, and three articles in the PBMB special issue on Soft Tissue Modelling.
• The community around SOFA is growing, with 175 people from 20 countries exchanging emails in the mailing-lists.
• While we do not know all labs and companies that are using or evaluating SOFA, there is at least one commercial laparoscopy simulator that should soon be available with SOFA in its core, created by Digital Trainers.
• The long awaited SOFA 1.0 release was not finalized, however much progress has been made and it should not keep you waiting much longer...

Videos

People

In 2010 we welcomed 5 new team members :

• Jerome Esnault is now working as an Engineer on extending Sofa for use in VR environments.
• Ahmed Yureidini started a PhD on parametric and implicit surface modeling of vasculature for real-time simulation of aneurysm embolization.
• Vincent Majorzyck started a PhD on fluid simulation and GPU.
• Hugo Talbot started a PhD on interactive simulation of cell resection through radio-frequency in the framework of cardiac arrhythmia.
• Ali Hamadi Dicko started a PhD with fundings from the ANR SoHuSim project.

7 people finished their contracts and left the SOFA team, but not necessarily the SOFA community :

• Michael Adam left in April after working as an engineer since 2006 on articulated rigid bodies. He also contributed many functionalities, among which the integration with Maya. He is now a R&D Engineer at 4D Views.
• Everton Hermann defended in June his PhD thesis "Interactive Physical Simulation on Multi-core and Multi-GPU Architectures". He is now working for Ubisoft, where he his applying to games the concepts he designed for Sofa parallelization.
• Christophe Guébert defended in July his PhD thesis "Simulation temps réel de suture de modèles déformables". He is now working for Digital Trainers, adapting his Sofa constraints modeling modules in the context the laparoscopy simulators.
• Florent Falipou left in August after working as an engineer since 2007. He added the support of the Ogre rendering engine, and also worked on GPU-based collisions, GUI tools, and many others. He took a R&D Engineer at the visual effects BUF Compagnie.
• Erik Pernod left in September after working as en engineer since 2008 on dynamic topologies and electro-physiology. He is now a R&D Freelance Engineer, working on a top-secret project, of which all I can say is that it is using Sofa in a new application domain.
• Olivier Comas defended just last month his PhD thesis "Real-time soft tissue modelling on GPU for medical simulation". He will soon move to Montreal to take a research associate position.
• Frédérick Roy left in December after working as an engineer since 2007. He mainly worked on the cataract surgery and interventional radiology simulations. He took a R&D Engineer position at Korea Institute of Science and Technology (KIST).

Some of their contributions are already available in the SVN version of SOFA, and other will make their way in the next release.

Code

While there has been no new release of Sofa, the development continued at a rapid pace. In 2010, 3379 commits where applied to the codebase, growing from 493K to 693K lines of code. Most of this code is already available in the public SVN (containing 456 KLOC, which is 56% more that the 291 KLOC in the beta 4 release), including :

• Parallelization with Kaapi
• OpenCL support
• Non-uniform hexahedral FEM
• VTK mesh import and export
• Tutorials

Publications

In 2010, the SOFA Team published 7 journal papers (including 1 SIGGRAPH paper and 3 papers in the PBMB special issue on soft tissue modelling) and 10 conference publications (including 2 MICCAI papers). We also know of at least 3 papers using Sofa that were published by other groups.

Journals

1. J. Allard, H. Courtecuisse, F. Faure. Implicit FEM Solver on GPU for Interactive Deformation Simulation. GPU Computing Gems Vol. 2, NVIDIA/Elsevier, July 2011. Book Chapter, to appear
2. Y. Wei, S. Cotin, J. Allard, L. Fang, C. Pan, S. Ma. Interactive Blood-Coil Simulation in Real-time during Aneurysm Embolization. Computers & Graphics, April 2011. Special issue on Visual Computing for Biology and Medicine, to appear
3. H. Courtecuisse, H. Jung, J. Allard, C. Duriez, D. Yong Lee, S. Cotin. GPU-based Real-Time Soft Tissue Deformation with Cutting and Haptic Feedback. Progress in Biophysics and Molecular Biology 103, 2-3, pp. 159-168, December 2010. Special Issue on Soft Tissue Modelling DOI
4. S. Marchesseau, T. Heimann, S. Chatelin, R. Willinger, H. Delingette. Fast porous visco-hyperelastic soft tissue model for surgery simulation: Application to liver surgery. Progress in Biophysics and Molecular Biology 103, 2-3, pp. 185-196, December 2010. Special Issue on Soft Tissue Modelling DOI
5. L. Jerabkova, G. Bousquet, S. Barbier, F. Faure, J. Allard. Volumetric Modeling and Interactive Cutting of Deformable Bodies. Progress in Biophysics and Molecular Biology 103, 2-3, pp. 217-224, December 2010. Special Issue on Soft Tissue Modelling DOI
6. C. Picard, C. Frisson, F. Faure, G. Drettakis, P. Kry. Advances in Modal Analysis Using a Robust and Multiscale Method. EURASIP Journal on Advances in Signal Processing 2010, December 2010. Special issue on Digital Audio Effects DOI
7. C. Öhman, D. M. Espino, T. Heinmann, M. Baleani, H. Delingette, M. Viceconti. Subject-specific knee joint model: Design of an experiment to validate a multi-body finite element model. The Visual Computer, November 2010. To appear DOI
8. J. Allard, F. Faure, H. Courtecuisse, F. Falipou, C. Duriez, P. G. Kry. Volume Contact Constraints at Arbitrary Resolution. ACM Transactions on Graphics (Proceedings of SIGGRAPH 2010) 29, 3, August 2010. DOI project
9. M. Nesme, F. Faure, Y. Payan. Accurate Interactive Animation of Deformable Models at Arbitrary Resolution. International Journal of Image and Graphics (IJIG) 10, 2, pp. 175-202, April 2010. DOI

Conferences

1. E. Dumortier, S. Cotin, C. Duriez, J. Allard, J. Dequidt, J. Rouland. Computer-based Training System for Cataract Surgery. International ICST Conference on Electronic Healthcare for the 21st century (eHealth), December 2010. Medical Conference
2. H. Courtecuisse, J. Allard, C. Duriez, S. Cotin. Asynchronous Preconditioners for Efficient Solving of Non-linear Deformations. Proceedings of Virtual Reality Interaction and Physical Simulation (VRIPHYS), November 2010. project
3. Y. Wei, L. Fang, S. Cotin, S. Ma. Interactive Blood-Coil Simulation using Discrete Exterior Calculus. International Conference on Vortex Flows and Vortex Models (ICVFM), November 2010.
4. S. Marchesseau, T. Heimann, S. Chatelin, R. Willinger, H. Delingette. Multiplicative Jacobian Energy Decomposition Method for Fast Porous Visco-Hyperelastic Soft Tissue Model. Proceedings of the International Conference on Medical Image Computing and Computer Assisted Intervention (MICCAI), LNCS 6361, pp. 235-242, September 2010. DOI
5. E. Hermann, B. Raffin, F. Faure, T. Gautier, J. Allard. Multi-GPU and Multi-CPU Parallelization for Interactive Physics Simulations. Euro-Par 2010, LNCS 6272, pp. 235-246, September 2010. DOI
6. O. Comas, C. Duriez, S. Cotin. Shell Model for Reconstruction and Real-Time Simulation of Thin Anatomical Structures. Proceedings of the International Conference on Medical Image Computing and Computer Assisted Intervention (MICCAI), LNCS 6362, pp. 371-379, September 2010. DOI
7. E. Pernod, M. Sermesant, J. Relan, H. Delingette. Interactive real time simulation of cardiac radio-frequency ablation. Proceedings of Eurographics Workshop on Visual Computing for Biology and Medicine (VCBM), July 2010. Best paper award DOI
8. H. Jung, S. Cotin, C. Duriez, J. Allard, D. Yong Lee. High Fidelity Haptic Rendering for Deformable Objects Undergoing Topology Changes. EuroHaptics 2010, LNCS 6191, pp. 262-268, July 2010. DOI
9. N. Boubchir, S. Cotin, O. Comas, F. Roy, M. Sanz, C. Duriez, J. Dequidt, J. Allard, J.-F. Rouland. Computer-Based Simulation of Cataract Surgery: Toward a New Teaching Paradigm. Annual Meeting of the Association for Research in Vision and Opthalmology, May 2010. Medical Conference
10. O. Comas, C. Duriez, S. Cotin. A Shell Model for Real-Time Simulation of Intra-ocular Implant Deployment. Proceedings of International Symposium on Biomedical Simulation (ISBMS), LNCS 5958, pp. 160-170, January 2010. DOI

PhD Theses

1. E. Hermann. Interactive Physical Simulation on Multi-core and Multi-GPU Architectures. Institut National Polytechnique de Grenoble (INPG), June 2010. project
2. C. Guébert. Simulation temps réel de suture de modèles déformables. Université de Lille, July 2010. project
3. O. Comas. Real-time soft tissue modelling on GPU for medical simulation. Université de Lille, December 2010. project

SOFA Users

1. L. Bibin, J. Anquez, J. P. de la Plata Alcalde, T. Boubekeur, E. D. Angelini, I. Bloch - Télécom ParisTech, Paris, France. Whole-Body Pregnant Woman Modeling By Digital Geometry Processing With Detailed Uterofetal Unit Based on Medical Images. IEEE Transactions on Biomedical Engineering 57, 10, October 2010. DOI
2. S.-L. Lee, A. Chung, M. Lerotic, M. A. Hawkins, D. Tait, G.-Z. Yang - Imperial College London, UK. Dynamic Shape Instantiation for Intra-operative Guidance. Proceedings of the International Conference on Medical Image Computing and Computer Assisted Intervention (MICCAI), LNCS 6361, pp. 69-76, September 2010. DOI
3. S. Ullrich, O. Grottke, R. Rossaint, M. Staat, T. M. Deserno, T. Kuhlen - Virtual Reality Group, RWTH Aachen University, Germany. Virtual Needle Simulation with Haptics for Regional Anaesthesia. IEEE Virtual Reality, Workshop on Medical Virtual Environments, March 2010.

SOFA project - (C) INRIA 2007-2011